Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsnpx agentmods add skills/k-dense-ai/scientific-agent-skills/scientific-critical-thinkingWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/scientific-critical-thinking)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/scientific-critical-thinking"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/scientific-critical-thinking/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/scientific-critical-thinking"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/scientific-critical-thinking.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00063 | $0.02047 |
| Opus 5 | $0.00032 | $0.01024 |
| Sonnet 5 | $0.00013 | $0.00409 |
| Haiku 4.5 | $0.00006 | $0.00205 |
Grade A, and why
scientific-critical-thinking scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured today.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 198 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Scientific Critical Thinking
Overview
Critical thinking is a systematic process for evaluating scientific rigor. Assess methodology, experimental design, statistical validity, biases, confounding, and evidence quality using GRADE and Cochrane ROB frameworks. Apply this skill for critical analysis of scientific claims.
When to Use This Skill
This skill should be used when:
- Evaluating research methodology and experimental design
- Assessing statistical validity and evidence quality
- Identifying biases and confounding in studies
- Reviewing scientific claims and conclusions
- Conducting systematic reviews or meta-analyses
- Applying GRADE or Cochrane risk of bias assessments
- Providing critical analysis of research papers
Visual Aids (Optional)
Only add figures when the user explicitly requests a diagram (for example, a GRADE flowchart, bias decision tree, or evidence-quality framework).
When figures help:
- Critical thinking framework diagrams
- Bias identification decision trees
- Evidence quality assessment flowcharts
- GRADE or risk-of-bias evaluation frameworks
How to create figures:
- Preferred: Use the scientific-schematics skill for AI-generated diagrams from a natural-language description
- Alternative: Build figures in your usual tools (draw.io, PowerPoint, matplotlib, etc.)
Run from the repository root, with OPENROUTER_API_KEY set:
python skills/scientific-schematics/scripts/generate_schematic.py "GRADE evidence assessment flowchart with downgrade and upgrade factors" -o figures/grade_flowchart.png --doc-type report
Disclosure: AI schematic generation sends your prompt to OpenRouter (a third-party API). Do not include unpublished sensitive details unless that transmission is appropriate for your project.
Core Capabilities
Seven capability areas, each with the questions to ask and what the answers imply, are in references/core_capabilities.md:
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- today Changed b77ba9ed1872
- 9d ago First seen · 198 lines · 63 tokens per session scan A 20880f5c2c2a
scientific-critical-thinking is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,469 stars, last pushed yesterday), licensed MIT. It adds 63 tokens to every session and 2,047 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
discovery-toolbox
A routed repertoire of 90 scientific thinking operators for biological research agents - visual reasoning, detectability and information budgets, search reframing, causal identification, competing explanations, observation and selection processes, pipeline artifact diagnosis, effort allocation, and confirmation…
discovery-director
Operate as a research director making original discoveries from a given biological question and dataset. Use when the task is open-ended scientific research, exploring omics or experimental data for findings, hypothesis generation and testing, screening a large candidate space of genes, variants, features or…
bio-interdomain-hgt
Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when studying lateral gene transfer, virus-host gene exchange, endogenous viral elements, or donor direction.
polars-dovmed
Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries should run through the hosted API or local parquet indexes.
csag-extraction
Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.
exploratory-data-analysis
Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.